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During the 1970s, Flanagan was a proponent of pyramid power.[6] He wrote several books and promoted it with lectures and seminars.[7] According to Flanagan, pyramids with the exact relative dimensions of Egyptian pyramids act as "an effective resonator of randomly polarized microwave signals which can be converted into electrical energy." [8] One of his first books, Pyramid Power, was featured in the lyrics of The Alan Parsons Project album, Pyramid.[9]

In 1958, at the age of 13, Flanagan invented the Neurophone, which he said transmitted sound via the nervous system to the brain.[10]Life magazine[11] called him a "unique, mature and inquisitive scientist". In 1968, the invention was improved by the development of a means of simplifying speech waveforms, for which he received a patent.[12]

In 1982, Flanagan and his wife, Gael Crystal, were credited with the discovery of a new form of colloidal silica, known as a microcluster, in the glacial water consumed by the Hunza people of northern Pakistan. The Flanagans then sold a product utilizing the microclusters called Crystal Energy (the ingredients are water, silica, potassium carbonate, and magnesium sulfate), which they say lowers the surface tension of drinking water.[13]